At Fios, oncology has always been a predominant research area with over 30% of our projects every year having a focus on oncology. Our team have extensive experience in analysing cancer research datasets, either pre-clinical or clinical, that are either generated in-house or datasets from publicly available databases such as CCLE, TCGA and DepMap. We can then integrate survival and other collected data into our analyses.
How We Can Help Your Oncology Research
By combining our expertise in bioinformatics analysis with our extensive knowledge in the oncology area, we can support your research at every stage of the drug development process from pre-clinical to clinical. Our bioinformatics services can help with:
- Target and lead identification and validation
- Identifying biomarkers for measurement of drug efficacy and mechanism of action
- Predicting biomarkers for stratification/classification of patient response to drug
- SNP genotype analysis & DNA sequence analysis for the detection of novel SNPs implicated in disease or response to drugs.
Our bespoke solutions utilise state-of-art approaches, tailored to the data types and requirements of each project.
Example Bioinformatics Analysis Report for Oncology Research
In this report review we summarise the main findings from our public bioinformatics analysis report: Immunological phenotype, response to therapy and survival.
Every time our clients work with us, they benefit from:
- A dedicated analyst backed by an experienced team to curate all data, identify the most appropriate statistical approach to take and provide a biological interpretation of results.
- An interactive data analysis report, internally peer-reviewed, including all analysis methods and results.
- Post-report follow ups: upon receipt of our data analysis report, we arrange a teleconference so that our lead analyst can talk through the results.
- Access to large capacity computing and secure data storage facilities.
Selected Projects We Supported
- Single-cell RNAseq analysis of a publicly available dataset, where normal and malignant epithelial cells were identified from transcriptome profiles of ~200,000 single cells from non-small cell lung cancer (NSCLC) patients.
- Associating copy number variants with cancer cell line gene dependency.
- Analysis of gene expression and mutation data from patient-derived xenograft models to select optimal models for testing.
- Associating drug response with changes in expression profiles to identify potential mechanisms of response to treatment.
- Investigation of drug or gene knockout-induced changes to the proteome of cancer cells or tissues from various model organisms.
Selected Publications
- CDK4/6 inhibition enhances antitumor efficacy of chemotherapy and immune checkpoint inhibitor combinations in preclinical models and enhances T-cell activation in patients with SCLC receiving chemotherapy
- Development of a gene expression–based prognostic signature for IDH wild-type glioblastoma
- Tumor Fusion Burden as a Hallmark of Immune Infiltration in Prostate Cancer
- Trilaciclib plus chemotherapy versus chemotherapy alone in patients with metastatic triple-negative breast cancer: a multicentre, randomised, open-label, phase 2 trial
- TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells
For more publications, visit our dedicated Publications page.
We were very pleased with the service provided by Fios Genomics. In particular, the Fios team were flexible and willing to spend time understanding our specific project needs and the key scientific questions we were asking of the experiments. They tailored the data output in a way that specifically addressed these questions, which was really helpful. The data package was Web-based and interactive and we were delighted with the way it was presented and explained to us. We will certainly work again with the Fios team for any future projects.
Case Study: Transcriptome Profiling in Multiple Tumour Types
The aim of this study was to exploit the publicly available datasets of The Cancer Genome Atlas (TGCA), PanCanAtlas, and Cancer Cell Line Encyclopaedia (CCLE) in order to extend transcriptomic and prognostic profiling of specific genes of interest in 33 tumour types across over 10,000 cancer patient samples and cell lines.
Webinar: Tumor fusion burden and the immune landscape of prostate cancer
We discuss how immune checkpoint inhibitors have been largely unsuccessful against prostate cancer, and how current biomarkers do not effectively identify those patients most likely to respond to treatment.
Data Analysis Report for Oncology
Our team has created a sample report based on data published from a study from Genentech, Inc. that Fios Genomics has been involved in.
This study, investigating response to PD-L1 blockade therapies in patients with metastatic urothelial cancers, has been published in Nature.
At Fios Genomics, we are completely data driven. Whatever your research area, we offer support at every stage of your research and for different purposes:
Discovery
Selecting the correct targets and/or the correct indication is essential for development success. We help support the process with robust analysis of historic or new data.
Preclinical Research
We help in experimental design and statistical analysis and guide our clients in making informed decisions during the preclinical stage.
Clinical
Research
We offer a comprehensive analysis approach for augmenting clinical trial outcomes, ensuring you get the most information out of your research.
Drug Repurposing
We have strong experience with identifying in silico new potential indications for existing drugs, reducing the cost and time of downstream wet lab validation.
